A general-purpose biomedical AI agent capable of executing complex research workflows using over 150 tools and databases.
Biomni is a "General-Purpose" biomedical agent. Unlike specialized skills (e.g., just for folding proteins), Biomni acts as a high-level orchestrator that can break down complex open-ended research questions into solvable sub-tasks using a vast library of tools.
When to Use This Skill
Complex Questions: "What are the potential drug targets for Alzheimer's related to mitochondrial dysfunction?"
Multi-Step Research: Tasks requiring literature search, data retrieval, and analysis in sequence.
Exploratory Analysis: When the exact path to the answer isn't known and requires "reasoning."
Core Capabilities
Tool Use: Access to 150+ tools, 105 software packages, and 59 databases.
Hypothesis Generation: Can formulate scientific hypotheses and plan experiments to test them.
Plan & Execute: Breaks down queries into a dependency graph of tasks.
Database QA: High accuracy (74.4%) in querying biomedical databases.
Workflow
Query Parsing: The agent analyzes the user's natural language request.
Tool Selection: It selects relevant tools (e.g., "Search GWAS Catalog", "Run GO Enrichment", "Fetch Uniprot Data").
Execution Loop:
Step 1: Get data.
Step 2: Analyze data.
Step 3: Refine plan based on intermediate results.
Synthesis: Combines all findings into a comprehensive answer.
Example Usage
User: "Identify genes associated with Type 2 Diabetes that are also expressed in the pancreas and have approved drugs."
Agent Action:
Tool: OpenTargets -> Get T2D associated genes.
Tool: GTEx -> Filter for high expression in Pancreas.
Tool: DrugBank -> Intersect with drug targets.
Result: Returns a list of genes (e.g., GLP1R, DPP4) and their drugs.
1---2name: biomni-research-agent3description: Bio-Research Generalist4license: MIT5---67<!--8# COPYRIGHT NOTICE9# This file is part of the "Universal Biomedical Skills" project.10# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>11# All Rights Reserved.12#13# This code is proprietary and confidential.14# Unauthorized copying of this file, via any medium is strictly prohibited.15#16# Provenance: Authenticated by MD BABU MIA1718-->192021# Biomni (General Biomedical Agent)2223A general-purpose biomedical AI agent capable of executing complex research workflows using over 150 tools and databases.2425Biomni is a "General-Purpose" biomedical agent. Unlike specialized skills (e.g., just for folding proteins), Biomni acts as a high-level orchestrator that can break down complex open-ended research questions into solvable sub-tasks using a vast library of tools.2627## When to Use This Skill2829* **Complex Questions**: "What are the potential drug targets for Alzheimer's related to mitochondrial dysfunction?"30* **Multi-Step Research**: Tasks requiring literature search, data retrieval, and analysis in sequence.31* **Exploratory Analysis**: When the exact path to the answer isn't known and requires "reasoning."3233## Core Capabilities34351. **Tool Use**: Access to 150+ tools, 105 software packages, and 59 databases.362. **Hypothesis Generation**: Can formulate scientific hypotheses and plan experiments to test them.373. **Plan & Execute**: Breaks down queries into a dependency graph of tasks.384. **Database QA**: High accuracy (74.4%) in querying biomedical databases.3940## Workflow41421. **Query Parsing**: The agent analyzes the user's natural language request.432. **Tool Selection**: It selects relevant tools (e.g., "Search GWAS Catalog", "Run GO Enrichment", "Fetch Uniprot Data").443. **Execution Loop**:45 * Step 1: Get data.46 * Step 2: Analyze data.47 * Step 3: Refine plan based on intermediate results.484. **Synthesis**: Combines all findings into a comprehensive answer.4950## Example Usage5152**User**: "Identify genes associated with Type 2 Diabetes that are also expressed in the pancreas and have approved drugs."5354**Agent Action**:551. Tool: `OpenTargets` -> Get T2D associated genes.562. Tool: `GTEx` -> Filter for high expression in Pancreas.573. Tool: `DrugBank` -> Intersect with drug targets.584. Result: Returns a list of genes (e.g., *GLP1R*, *DPP4*) and their drugs.5960<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add bg-szy/biomni-research-agent in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
Bio-Research Generalist It is listed under AI & ML on SkillMD.
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bg-szy (@bg-szy) published this skill. Their other Agent Skills are listed on their SkillMD profile.
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